## [1] "Max fold diff lib size = 1.75956241223834"

## [1] "57820 total transcripts. Keeping 17782 transcripts after filtering"

QC checks

Heirarchical clustering

Heirarchical clustering based on expression profile Spearman correlations. This shows that the data are overall high quality (no outliers), with good grouping of samples within-cell lines. The biggest difference is clearly between colon and ovarian cell lines.

Multi-dimensional scaling

PCA

lCPM distributions

Comparing distribution of log-counts per million per sample looks reasonable

Replicate correlations

Comparing BIRC6 expression levels

## `summarise()` has grouped output by 'samp_pert', 'cell_line'. You can override
## using the `.groups` argument.
## # A tibble: 6 × 4
## # Groups:   samp_pert, cell_line [6]
##   samp_pert        cell_line perturbation BIRC6_GE
##   <chr>            <chr>     <chr>           <dbl>
## 1 HCC15.sgBIRC6.1  HCC15     sgBIRC6.1        5.68
## 2 HCC15.sgBIRC6.4  HCC15     sgBIRC6.4        5.61
## 3 HCC15.sgCh2.2    HCC15     sgCh2.2          6.66
## 4 HCC202.sgBIRC6.1 HCC202    sgBIRC6.1        6.16
## 5 HCC202.sgBIRC6.4 HCC202    sgBIRC6.4        5.78
## 6 HCC202.sgCh2.2   HCC202    sgCh2.2          7.00

Collapse replicates

Save LCPM data (rep collapsed)

Diff expression analysis

Collapse across replicates by summing read counts Model cell line as random effect

DE in BIRC6 Dependent lines

## 
## Attaching package: 'scales'
## The following object is masked from 'package:readr':
## 
##     col_factor
## 
## Attaching package: 'ggthemes'
## The following object is masked from 'package:cowplot':
## 
##     theme_map

GSEA

## [1] "Running gene-permutation testing with 1000000 perms"

## [1] "Running gene-permutation testing with 1000000 perms"

## [1] "Running gene-permutation testing with 1000000 perms"

DE in BIRC6 Independent lines

GSEA

## [1] "Running gene-permutation testing with 1000000 perms"

## [1] "Running gene-permutation testing with 1000000 perms"

## [1] "Running gene-permutation testing with 1000000 perms"

Comparison of DE in Dependent vs Independent lines

Estimated KO effect in Dependent - Independent lines

GSEA

## [1] "Running gene-permutation testing with 1000000 perms"

## [1] "Running gene-permutation testing with 1000000 perms"

## [1] "Running gene-permutation testing with 1000000 perms"

Average DE across all cell lines

GSEA

## [1] "Running gene-permutation testing with 1000000 perms"

## [1] "Running gene-permutation testing with 1000000 perms"

## [1] "Running gene-permutation testing with 1000000 perms"

#model individual cell line effects

GSEA

## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.